MeshCAM does flip as a loop (somersault) rather than barrel roll. (notice the “horns” facing the front on the first side machining and facing the rear on the second side machining) That is what makes the two-pin “fence” and one-pin endstop so nice to use. The geometry doesn’t even need to be centered in the stock in either direction. Just measure the “good” edges of the stock and enter that Y size, and a reasonable X size for the stock into MeshCAM and lock the stock size. As long as the stock is generally the right size to fit the geometry, most of it can be just rough-cut.
The thickness does need to be uniform and accurately measured and entered for the two-sided job since that is the only thing that relates the Z position of the first and second side machining.
But as I said, I know now I was a little too agressive on the roughing settings. I wasn’t in the room the whole time of the cutting, and did hear some funky noises at a couple of points. After some X step skipping, the cutter would have been encountering a big vertical wall it didn’t expect to be there, instead of the little .020" vertical bite it was expecting.